I.Data origine (Mus musculus - tibialis anterior muscle)

In order to explore cell expression during muscle regeneration in young(2-3 months) and old(18-22 months) cells, RNAseq experiments were performed using cells sorted and FACs at four time points:

  • D0 muscles without injury
  • D2, 2 days after cardiotoxin-induced injury
  • D4, 4 days after injury
  • D7, 7 days after injury

The cell types sampled were as follows:

  • D0 , Endothelial Cells ECs, FibroAdipogenic Progenitors - FAPs, Muscle Stem Cells MuSCs.
  • D2 , ECs, FAPs, MuSCs., Neutrophile Cells, Inflammatory Macrophages - Inflammatory-Mac and Resolving Macrophages - Resolving-Mac .
  • D4, ECs, FAPs, MuSCs, Inflammatory-Mac, Resolving-Mac
  • D7, ECs, FAPs, MuSCs, Resolving-Mac

I.1 Pretreatment RNA-seq data with pipeline nfcore/rnaseq (v.1.4.2)

The RNA-seq data is aligned to the GRCm38 genome with STAR and counted with FeatureCount .

Only transcripts associated with coding proteins are kept.

Differentially expressed genes (DEG) processed with DESeq2_1.30.1 old vs young (reference expression is young one), for each cell type at each time Day_TypeCell_Old vs Day_TypeCell_Young

II.Overview of DEG significant analysis

On any given day and cell type there are 4499 genes differentilly expressed with a good confidence (padj<=0.05) (= DEG significative) on 17797 genes expressed in total or 25% of DEG significant.

The table below, is the percent of DEG significant on total genes expressed. ## Percent DEG significant table
D0 D2 D4 D7 PercentDEGSigniOnTyCell
ECs 2 1.3 6.2 13.7 19.1
FAPs 11.5 5.3 8.7 9.1 25.9
MuSCs 10.6 42.3 30.7 13.3 72.8
Inflammatory-Mac NA 0.7 0.4 NA 1
Neutrophils NA 6.9 NA NA 6.9
Resolving-Mac NA 2.1 0.8 3.1 5.3
PercentDEGSigniOnDay 21.7 54.1 42.2 32.8 NA

Number DEG significant table

Graphics and tables are in /home/bioinfo/BulkAnalysis_plusNetwork/exam_INTER_conditions/static/

III.Exploration of DEG significant patterns in one type cell on muscle repair

This exploration is type cell specific and focus on gene differentially expressed significant (padj<0.05) On one type Cell, we observe different dynamics of differential expression across days

  • For some gene, the difference between Old and Young are specific of one day, on one step of muscle regeneration.
  • For some gene, the difference is always present, no specific.
  • For some gene, the age up his expression in some days and down in other day.
one.Day two.Day three.Day four.Day
Number Gene DE on 4489 1170 208 35
Pourcent Gene DE on 76 20 4 0

III.1 Sankey plot - Show the days pattern of DEG

Group by number of day DEG significant

Group by combination of days DEG significant

III.2 Sankey plot - Show the days pattern of DEG UP and DOWN significant

ECs

Group by combination of number of days DEG UP and DOWN significant

Group by number of day DEG UP and DOWN significant

Group by combination of days DEG UP and DOWN significant

Table with pattern the most present

FAPs

Group by combination of number of days DEG UP and DOWN significant

Group by number of day DEG UP and DOWN significant

Group by combination of days DEG UP and DOWN significant

Table with pattern the most present

MuSCs

Group by combination of number of days DEG UP and DOWN significant

Group by number of day DEG UP and DOWN significant

Group by combination of days DEG UP and DOWN significant

Table with pattern the most present

Inflammatory-Mac

Group by combination of number of days DEG UP and DOWN significant

Group by number of day DEG UP and DOWN significant

Group by combination of days DEG UP and DOWN significant

Table with pattern the most present

Resolving-Mac

Group by combination of number of days DEG UP and DOWN significant

Group by number of day DEG UP and DOWN significant

Group by combination of days DEG UP and DOWN significant

Table with pattern the most present

IV. Total table gene differential express significant

linksTableUpDown

V. Next report on genes set enrichment

linksreportgsea